# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:54:45 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(c(cn1)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 SD5  SD5  5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine  ligand  50  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SD5
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 SD5  N01   N  NH2   0  -0.833   5.2237   3.4309  -0.9128
 SD5  C02   C  CR6   0   0.495   4.0895   2.7623  -0.6089
 SD5  C03   C  CR16  0  -0.431   4.1034   1.7044   0.3219
 SD5  C04   C  CR6   0  -0.127   2.9398   1.0156   0.5714
 SD5  C05   C  CR6   0  -0.039   1.7596   1.3759  -0.1010
 SD5  C06   C  CR16  0  -0.085   1.8641   2.4471  -0.9780
 SD5  N07   N  N     0  -0.449   2.9725   3.1232  -1.2345
 SD5  C08   C  CR6   0   0.228   0.4561   0.6912   0.0281
 SD5  C09   C  CR16  0  -0.493  -0.6866   1.4339   0.2465
 SD5  C10   C  CR6   0   0.592  -1.8988   0.7131   0.3055
 SD5  N11   N  N     0  -0.545  -1.8916  -0.6128   0.2003
 SD5  C12   C  CR6   0   0.630  -0.7295  -1.2291  -0.0021
 SD5  N13   N  N     0  -0.516   0.4577  -0.6314  -0.1114
 SD5  N14   N  NT    0  -0.517  -0.7616  -2.5810  -0.1291
 SD5  C15   C  CH2   0  -0.321  -1.9600  -3.3538   0.1245
 SD5  C16   C  CH2   0  -0.184  -2.0507  -4.4949  -0.8719
 SD5  O17   O  O2    0  -0.485  -0.8876  -5.2924  -0.8639
 SD5  C18   C  CH2   0  -0.186   0.2545  -4.5222  -1.1671
 SD5  C19   C  CH2   0  -0.313   0.4451  -3.3810  -0.1844
 SD5  N20   N  NT    0  -0.515  -3.1037   1.3122   0.4639
 SD5  C21   C  CH2   0  -0.327  -4.3007   0.5402   0.7510
 SD5  C22   C  CH2   0  -0.188  -5.4994   1.1646   0.0637
 SD5  O23   O  O2    0  -0.482  -5.6519   2.5229   0.4111
 SD5  C24   C  CH2   0  -0.181  -4.5052   3.2578   0.0549
 SD5  C25   C  CH2   0  -0.320  -3.2540   2.7284   0.7357
 SD5  C26   C  CT    0   1.072   2.9755  -0.0855   1.6003
 SD5  F27   F  F     0  -0.307   3.1333  -1.2891   1.0433
 SD5  F28   F  F     0  -0.306   3.9995   0.0724   2.4508
 SD5  F29   F  F     0  -0.305   1.8701  -0.1160   2.3467
 SD5  HN01  H  HNH2  0   0.394   5.1377   4.3042  -1.4050
 SD5  HN0A  H  HNH2  0   0.402   6.0271   3.3410  -0.3152
 SD5  H03   H  HCR6  0   0.287   5.0258   1.4674   0.8337
 SD5  H06   H  HCR6  0   0.268   0.9816   2.7645  -1.5241
 SD5  H09   H  HCR6  0   0.269  -0.6203   2.5003   0.3905
 SD5  H15   H  HCH2  0   0.229  -1.9416  -3.7520   1.1474
 SD5  H15A  H  HCH2  0   0.276  -2.8376  -2.7191   0.0340
 SD5  H16   H  HCH2  0   0.240  -2.8924  -5.1414  -0.6194
 SD5  H16A  H  HCH2  0   0.204  -2.2286  -4.0852  -1.8764
 SD5  H18   H  HCH2  0   0.240   1.1176  -5.1883  -1.1303
 SD5  H18A  H  HCH2  0   0.204   0.1837  -4.1146  -2.1857
 SD5  H19   H  HCH2  0   0.272   1.2837  -2.7651  -0.4949
 SD5  H19A  H  HCH2  0   0.226   0.6769  -3.7808   0.8115
 SD5  H21   H  HCH2  0   0.281  -4.1713  -0.4808   0.4033
 SD5  H21A  H  HCH2  0   0.234  -4.4683   0.5044   1.8350
 SD5  H22   H  HCH2  0   0.208  -5.3934   1.0555  -1.0248
 SD5  H22A  H  HCH2  0   0.243  -6.4082   0.6436   0.3680
 SD5  H24   H  HCH2  0   0.208  -4.3572   3.2365  -1.0340
 SD5  H24A  H  HCH2  0   0.246  -4.6701   4.2942   0.3522
 SD5  H25   H  HCH2  0   0.240  -3.3092   2.9037   1.8170
 SD5  H25A  H  HCH2  0   0.266  -2.4062   3.2909   0.3530

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 SD5  N01  C02   single    1.351  0.020  1.351
 SD5  N01  HN01  single    0.890  0.020  1.040
 SD5  N01  HN0A  single    0.890  0.020  1.040
 SD5  C03  C02   aromatic  1.409  0.020  1.409
 SD5  C02  N07   aromatic  1.330  0.020  1.330
 SD5  C03  C04   aromatic  1.375  0.020  1.375
 SD5  C03  H03   single    0.930  0.020  1.080
 SD5  C26  C04   single    1.507  0.020  1.507
 SD5  C04  C05   aromatic  1.405  0.020  1.405
 SD5  C05  C08   single    1.478  0.020  1.478
 SD5  C05  C06   aromatic  1.388  0.020  1.388
 SD5  N07  C06   aromatic  1.324  0.020  1.324
 SD5  C06  H06   single    0.930  0.020  1.080
 SD5  C09  C08   aromatic  1.380  0.020  1.380
 SD5  C08  N13   aromatic  1.330  0.020  1.330
 SD5  C09  C10   aromatic  1.412  0.020  1.412
 SD5  C09  H09   single    0.930  0.020  1.080
 SD5  N20  C10   single    1.355  0.020  1.355
 SD5  C10  N11   aromatic  1.330  0.020  1.330
 SD5  N11  C12   aromatic  1.331  0.020  1.331
 SD5  N13  C12   aromatic  1.334  0.020  1.334
 SD5  C12  N14   single    1.358  0.020  1.358
 SD5  N14  C19   single    1.449  0.020  1.449
 SD5  N14  C15   single    1.448  0.020  1.448
 SD5  C15  C16   single    1.518  0.020  1.518
 SD5  C15  H15   single    0.970  0.020  1.090
 SD5  C15  H15A  single    0.970  0.020  1.090
 SD5  C16  O17   single    1.410  0.020  1.410
 SD5  C16  H16   single    0.970  0.020  1.090
 SD5  C16  H16A  single    0.970  0.020  1.090
 SD5  C18  O17   single    1.410  0.020  1.410
 SD5  C19  C18   single    1.518  0.020  1.518
 SD5  C18  H18   single    0.970  0.020  1.090
 SD5  C18  H18A  single    0.970  0.020  1.090
 SD5  C19  H19   single    0.970  0.020  1.090
 SD5  C19  H19A  single    0.970  0.020  1.090
 SD5  C25  N20   single    1.450  0.020  1.450
 SD5  N20  C21   single    1.453  0.020  1.453
 SD5  C21  C22   single    1.516  0.020  1.516
 SD5  C21  H21   single    0.970  0.020  1.090
 SD5  C21  H21A  single    0.970  0.020  1.090
 SD5  O23  C22   single    1.410  0.020  1.410
 SD5  C22  H22   single    0.970  0.020  1.090
 SD5  C22  H22A  single    0.970  0.020  1.090
 SD5  C24  O23   single    1.408  0.020  1.408
 SD5  C25  C24   single    1.520  0.020  1.520
 SD5  C24  H24   single    0.970  0.020  1.090
 SD5  C24  H24A  single    0.970  0.020  1.090
 SD5  C25  H25   single    0.970  0.020  1.090
 SD5  C25  H25A  single    0.970  0.020  1.090
 SD5  F27  C26   single    1.336  0.020  1.336
 SD5  F29  C26   single    1.334  0.020  1.334
 SD5  C26  F28   single    1.340  0.020  1.340

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 SD5  HN0A  N01  HN01  115.90  3.000
 SD5  HN0A  N01  C02   119.52  3.000
 SD5  HN01  N01  C02   117.89  3.000
 SD5  N07   C02  C03   121.51  3.000
 SD5  N07   C02  N01   117.70  3.000
 SD5  C03   C02  N01   120.78  3.000
 SD5  H03   C03  C04   121.76  3.000
 SD5  H03   C03  C02   119.05  3.000
 SD5  C04   C03  C02   119.18  3.000
 SD5  C26   C04  C05   122.26  3.000
 SD5  C05   C04  C03   119.70  3.000
 SD5  C26   C04  C03   118.02  3.000
 SD5  C08   C05  C06   118.62  3.000
 SD5  C06   C05  C04   115.90  3.000
 SD5  C08   C05  C04   125.46  3.000
 SD5  H06   C06  N07   115.72  3.000
 SD5  H06   C06  C05   118.84  3.000
 SD5  N07   C06  C05   125.43  3.000
 SD5  C06   N07  C02   118.26  3.000
 SD5  N13   C08  C09   123.55  3.000
 SD5  N13   C08  C05   116.78  3.000
 SD5  C09   C08  C05   119.65  3.000
 SD5  H09   C09  C10   123.52  3.000
 SD5  H09   C09  C08   120.17  3.000
 SD5  C10   C09  C08   116.28  3.000
 SD5  N20   C10  N11   117.05  3.000
 SD5  N11   C10  C09   120.07  3.000
 SD5  N20   C10  C09   122.88  3.000
 SD5  C12   N11  C10   118.58  3.000
 SD5  N14   C12  N13   117.35  3.000
 SD5  N14   C12  N11   117.04  3.000
 SD5  N13   C12  N11   125.60  3.000
 SD5  C12   N13  C08   115.85  3.000
 SD5  C19   N14  C15   113.65  3.000
 SD5  C15   N14  C12   122.29  3.000
 SD5  C19   N14  C12   122.24  3.000
 SD5  H15A  C15  H15   107.63  3.000
 SD5  H15A  C15  C16   109.64  3.000
 SD5  H15   C15  C16   109.88  3.000
 SD5  H15A  C15  N14   110.00  3.000
 SD5  H15   C15  N14   110.05  3.000
 SD5  C16   C15  N14   109.61  3.000
 SD5  H16A  C16  H16   107.91  3.000
 SD5  H16A  C16  O17   110.45  3.000
 SD5  H16   C16  O17   107.45  3.000
 SD5  H16A  C16  C15   109.23  3.000
 SD5  H16   C16  C15   109.85  3.000
 SD5  O17   C16  C15   111.85  3.000
 SD5  C18   O17  C16   110.96  3.000
 SD5  H18A  C18  H18   107.97  3.000
 SD5  H18A  C18  C19   109.22  3.000
 SD5  H18   C18  C19   109.75  3.000
 SD5  H18A  C18  O17   110.45  3.000
 SD5  H18   C18  O17   107.46  3.000
 SD5  C19   C18  O17   111.90  3.000
 SD5  H19A  C19  H19   107.64  3.000
 SD5  H19A  C19  C18   109.88  3.000
 SD5  H19   C19  C18   109.77  3.000
 SD5  H19A  C19  N14   110.01  3.000
 SD5  H19   C19  N14   109.93  3.000
 SD5  C18   C19  N14   109.59  3.000
 SD5  C25   N20  C21   113.36  3.000
 SD5  C21   N20  C10   121.39  3.000
 SD5  C25   N20  C10   123.09  3.000
 SD5  H21A  C21  H21   107.68  3.000
 SD5  H21A  C21  C22   109.91  3.000
 SD5  H21   C21  C22   109.64  3.000
 SD5  H21A  C21  N20   109.77  3.000
 SD5  H21   C21  N20   109.75  3.000
 SD5  C22   C21  N20   110.05  3.000
 SD5  H22A  C22  H22   108.02  3.000
 SD5  H22A  C22  O23   107.53  3.000
 SD5  H22   C22  O23   110.49  3.000
 SD5  H22A  C22  C21   109.60  3.000
 SD5  H22   C22  C21   109.38  3.000
 SD5  O23   C22  C21   111.74  3.000
 SD5  C24   O23  C22   110.63  3.000
 SD5  H24A  C24  H24   107.99  3.000
 SD5  H24A  C24  C25   109.47  3.000
 SD5  H24   C24  C25   109.05  3.000
 SD5  H24A  C24  O23   107.69  3.000
 SD5  H24   C24  O23   110.50  3.000
 SD5  C25   C24  O23   112.05  3.000
 SD5  H25A  C25  H25   107.68  3.000
 SD5  H25A  C25  C24   107.71  3.000
 SD5  H25   C25  C24   110.16  3.000
 SD5  H25A  C25  N20   111.01  3.000
 SD5  H25   C25  N20   110.25  3.000
 SD5  C24   C25  N20   109.98  3.000
 SD5  F29   C26  F28   106.30  3.000
 SD5  F28   C26  F27   106.29  3.000
 SD5  F29   C26  F27   108.10  3.000
 SD5  F28   C26  C04   111.41  3.000
 SD5  F29   C26  C04   112.27  3.000
 SD5  F27   C26  C04   112.11  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 SD5  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 SD5  CONST_02  C05   C06  N07  C02     0.00   0.0  0
 SD5  CONST_03  C06   N07  C02  C03     0.00   0.0  0
 SD5  CONST_04  C08   C05  C04  C03   180.00   0.0  0
 SD5  CONST_05  C06   C05  C04  C03     0.00   0.0  0
 SD5  CONST_06  N07   C02  C03  C04     0.00   0.0  0
 SD5  CONST_09  N07   C06  C05  C04     0.00   0.0  0
 SD5  CONST_10  C10   C09  C08  C05   180.00   0.0  0
 SD5  CONST_11  C12   N13  C08  C05   180.00   0.0  0
 SD5  CONST_14  C08   C05  C06  N07   180.00   0.0  0
 SD5  CONST_15  N11   C10  C09  C08     0.00   0.0  0
 SD5  CONST_16  N11   C12  N13  C08     0.00   0.0  0
 SD5  CONST_17  C12   N13  C08  C09     0.00   0.0  0
 SD5  CONST_18  C12   N11  C10  C09     0.00   0.0  0
 SD5  CONST_19  N13   C08  C09  C10     0.00   0.0  0
 SD5  CONST_20  N13   C12  N11  C10     0.00   0.0  0
 SD5  CONST_21  N20   C10  C09  C08   180.00   0.0  0
 SD5  CONST_22  N14   C12  N13  C08   180.00   0.0  0
 SD5  CONST_23  N14   C12  N11  C10   180.00   0.0  0
 SD5  CONST_24  N20   C10  N11  C12   180.00   0.0  0
 SD5  CONST_25  C04   C03  C02  N01   180.00   0.0  0
 SD5  CONST_26  C06   N07  C02  N01   180.00   0.0  0
 SD5  CONST_27  C26   C04  C03  C02   180.00   0.0  0
 SD5  CONST_28  C26   C04  C05  C06   180.00   0.0  0
 SD5  CONST_29  C26   C04  C05  C08     0.00   0.0  0
 SD5  CONST_30  H06   C06  N07  C02   180.00   0.0  0
 SD5  CONST_31  H03   C03  C04  C05   180.00   0.0  0
 SD5  CONST_32  H09   C09  C08  C05     0.00   0.0  0
 SD5  CONST_33  HN01  N01  C02  C03   180.00   0.0  0
 SD5  Var_01    C25   N20  C10  C09    -7.06  30.0  2
 SD5  Var_02    C24   C25  N20  C10   145.30  30.0  1
 SD5  Var_03    C22   C21  N20  C10  -144.58  30.0  1
 SD5  Var_04    C19   N14  C12  N11  -172.10  30.0  2
 SD5  Var_05    C18   C19  N14  C12  -142.59  30.0  1
 SD5  Var_06    C16   C15  N14  C12   142.52  30.0  1
 SD5  Var_07    O17   C18  C19  N14   -54.62  30.0  1
 SD5  Var_08    O17   C16  C15  N14    54.75  30.0  1
 SD5  Var_09    C19   C18  O17  C16    58.61  30.0  1
 SD5  Var_10    O23   C24  C25  N20    54.47  30.0  1
 SD5  Var_11    O23   C22  C21  N20   -54.96  30.0  1
 SD5  Var_12    C25   C24  O23  C22   -59.02  30.0  1
 SD5  Var_13    F27   C26  C04  C03   -96.95  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SD5  plan-1  N01   0.020
 SD5  plan-1  C02   0.020
 SD5  plan-1  C03   0.020
 SD5  plan-1  C04   0.020
 SD5  plan-1  C05   0.020
 SD5  plan-1  C06   0.020
 SD5  plan-1  N07   0.020
 SD5  plan-1  C08   0.020
 SD5  plan-1  C26   0.020
 SD5  plan-1  H03   0.020
 SD5  plan-1  H06   0.020
 SD5  plan-2  C05   0.020
 SD5  plan-2  C08   0.020
 SD5  plan-2  C09   0.020
 SD5  plan-2  C10   0.020
 SD5  plan-2  N11   0.020
 SD5  plan-2  C12   0.020
 SD5  plan-2  N13   0.020
 SD5  plan-2  N14   0.020
 SD5  plan-2  N20   0.020
 SD5  plan-2  H09   0.020
 SD5  plan-3  N01   0.020
 SD5  plan-3  C02   0.020
 SD5  plan-3  HN01  0.020
 SD5  plan-3  HN0A  0.020

